Rosen’s (M,R) system in process algebra

Gatherer, D. and Galpin, V. (2013) Rosen’s (M,R) system in process algebra. BMC Systems Biology, 7(128), (doi:10.1186/1752-0509-7-128) (PMID:24237684) (PMCID:PMC3879122)

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Abstract

Background: Robert Rosen’s Metabolism-Replacement, or (M,R), system can be represented as a compact network structure with a single source and three products derived from that source in three consecutive reactions. (M,R) has been claimed to be non-reducible to its components and algorithmically non-computable, in the sense of not being evaluable as a function by a Turing machine. If (M,R)-like structures are present in real biological networks, this suggests that many biological networks will be non-computable, with implications for those branches of systems biology that rely on in silico modelling for predictive purposes.

Results: We instantiate (M,R) using the process algebra Bio-PEPA, and discuss the extent to which our model represents a true realization of (M,R). We observe that under some starting conditions and parameter values, stable states can be achieved. Although formal demonstration of algorithmic computability remains elusive for (M,R), we discuss the extent to which our Bio-PEPA representation of (M,R) allows us to sidestep Rosen’s fundamental objections to computational systems biology.

Conclusions: We argue that the behaviour of (M,R) in Bio-PEPA shows life-like properties.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gatherer, Dr Derek
Authors: Gatherer, D., and Galpin, V.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:BMC Systems Biology
Publisher:BioMed Central
ISSN:1752-0509
ISSN (Online):1752-0509
Copyright Holders:Copyright © 2013 The Authors
First Published:First published in BMC Systems Biology 7(128)
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
656321Genomics of human cytomegalovirusAndrew DavisonMedical Research Council (MRC)MC_UU_12014/3MVLS III - CENTRE FOR VIRUS RESEARCH